ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions

Abstract
ZINBA (Zero-Inflated Negative Binomial Algorithm) identifies genomic regions enriched in a variety of ChIP-seq and related next-generation sequencing experiments (DNA-seq), calling both broad and narrow modes of enrichment across a range of signal-to-noise ratios. ZINBA models and accounts for factors that co-vary with background or experimental signal, such as G/C content, and identifies enrichment in genomes with complex local copy number variations. ZINBA provides a single unified framework for analyzing DNA-seq experiments in challenging genomic contexts.
Software website: http://code.google.com/p/zinba/

Rashid, Naim UAffiliation: Department of Biostatistics, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill

Giresi, Paul GAffiliation: Department of Biology, University of North Carolina at Chapel Hill
Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill
Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill

Ibrahim, Joseph GAffiliation: Department of Biostatistics, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill

Sun, WeiAffiliation: Department of Biostatistics, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill
Department of Genetics, University of North Carolina at Chapel Hill
School of Medicine, University of North Carolina at Chapel Hill

Lieb, Jason DAffiliation: Department of Biology, University of North Carolina at Chapel Hill
Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill
Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill

Title

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions